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- PDB-8jfs: Phosphate bound acylphosphatase from Deinococcus radiodurans at 1... -

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Basic information

Entry
Database: PDB / ID: 8jfs
TitlePhosphate bound acylphosphatase from Deinococcus radiodurans at 1 Angstrom resolution
ComponentsAcylphosphatase
KeywordsHYDROLASE / phosphate bound acylphosphatase
Function / homology
Function and homology information


acylphosphatase / acylphosphatase activity
Similarity search - Function
Acylphosphatase / Acylphosphatase / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / Acylphosphatase-like domain superfamily
Similarity search - Domain/homology
CITRIC ACID / PHOSPHATE ION / Acylphosphatase
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsKhakerwala, Z. / Kumar, A. / Makde, R.D.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India) India
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Crystal structure of phosphate bound Acyl phosphatase mini-enzyme from Deinococcus radiodurans at 1 angstrom resolution.
Authors: Khakerwala, Z. / Kumar, A. / Makde, R.D.
History
DepositionMay 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acylphosphatase
B: Acylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3819
Polymers19,8682
Non-polymers5137
Water3,747208
1
A: Acylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2675
Polymers9,9341
Non-polymers3334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-31 kcal/mol
Surface area4790 Å2
MethodPISA
2
B: Acylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1144
Polymers9,9341
Non-polymers1803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-19 kcal/mol
Surface area4890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.003, 28.472, 83.604
Angle α, β, γ (deg.)90.000, 90.430, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acylphosphatase / Acylphosphate phosphohydrolase


Mass: 9934.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (radioresistant)
Strain: R1 / Gene: acyP, DR_0929 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta pLysS / References: UniProt: Q9RVU3, acylphosphatase

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Non-polymers , 5 types, 215 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.7 %
Description: it was a big crystal with irregular shape which broke into 2 pieces when transferred to paratone oil. one of the piece got diffracted other one was mosaic.
Crystal growTemperature: 293 K / Method: microbatch / pH: 4.2
Details: 0.1M Phosphate-citrate pH 4.2, 40% ethanol, 5% PEG 1000
Temp details: 291-293K fluctuation was there

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97777 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 21, 2022 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97777 Å / Relative weight: 1
ReflectionResolution: 1→33 Å / Num. obs: 82616 / % possible obs: 97.73 % / Redundancy: 6.7 % / Biso Wilson estimate: 9.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.017 / Rrim(I) all: 0.046 / Χ2: 0.94 / Net I/σ(I): 19.8
Reflection shellResolution: 1→1.02 Å / Redundancy: 6 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3883 / CC1/2: 0.881 / Rpim(I) all: 0.354 / Rrim(I) all: 0.637 / Χ2: 0.84 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDS1.12.13data reduction
Aimless0.7.8data scaling
PHASER1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→33 Å / SU ML: 0.0912 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.4441
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2046 1773 2.15 %
Rwork0.1927 80727 -
obs0.1929 82500 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.29 Å2
Refinement stepCycle: LAST / Resolution: 1→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1384 0 30 208 1622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00761542
X-RAY DIFFRACTIONf_angle_d1.13422109
X-RAY DIFFRACTIONf_chiral_restr0.0895218
X-RAY DIFFRACTIONf_plane_restr0.0111287
X-RAY DIFFRACTIONf_dihedral_angle_d12.6961230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.030.25971300.27185903X-RAY DIFFRACTION93.74
1.03-1.060.26041300.2515956X-RAY DIFFRACTION94.47
1.06-1.090.24751320.22996004X-RAY DIFFRACTION95.01
1.09-1.130.21691330.21516041X-RAY DIFFRACTION95.93
1.13-1.180.20461350.20776143X-RAY DIFFRACTION96.63
1.18-1.230.21951350.20046155X-RAY DIFFRACTION97.99
1.23-1.290.19281370.19996218X-RAY DIFFRACTION98.12
1.29-1.380.21221380.20416274X-RAY DIFFRACTION99.23
1.38-1.480.19991380.19396308X-RAY DIFFRACTION99.74
1.48-1.630.20171400.19016367X-RAY DIFFRACTION99.74
1.63-1.870.21021390.18676363X-RAY DIFFRACTION99.94
1.87-2.350.2021420.17976436X-RAY DIFFRACTION99.89
2.35-330.19071440.18176559X-RAY DIFFRACTION99.93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.147011942934.531117545670.08074107822534.761924983920.4851568961371.03486671687-0.07855979104540.151332391890.0266403739946-0.03725120519970.08770692705790.002798345156710.05493192109550.0242218882792-0.01763771548560.04820692922560.0149885096828-0.00216205388140.0502576392748-0.0132290920230.07774300247221.53006279148-1.391034444579.96867073458
22.621211843351.874430910010.9834800032172.52790334261.042705376411.652653647310.0445180111876-0.03562815194530.1182297270310.0520788943832-0.04569080650590.0600032269541-0.00828682996328-0.0598070412541-0.00166999417390.05277718193850.009546853457870.004708953575930.04587636866580.002808994248340.0456619934359-3.556609419185.7555655303610.2146731795
37.884546002774.057423900922.65901560854.269333279891.63178114791.09351208724-0.03488382928990.295912817853-0.1059856896680.09242312693850.207136504538-0.221846203320.01747178592550.123959125379-0.197361587320.05293838005370.01347303248310.001655050072410.0475839211375-0.01778055837940.06678491909645.368530095965.2506648715110.7828313083
44.597792230422.994605703742.001108704884.266356231591.269568796113.958319206120.240389769776-0.53288310768-0.1045789808870.337355685155-0.166701327115-0.09907826593570.211238109769-0.0660293907228-0.06278071582510.131854573404-0.00502101466044-0.01696206296860.117752400494-0.003849410044220.0643599228883.96151012663.6302729951620.8101956264
57.234426037461.62166030495-0.5115897418581.079097975830.06000182441450.592502474030.0943194964577-0.170643676781-0.3844094914110.114424385428-0.0861440576634-0.1365188565240.05058871124640.0433646102728-0.001620299752210.0718304020320.00749644064244-2.99646562882E-50.05464842302690.001591831570090.0860098434504-1.77098689737-3.2767065346114.0822303979
66.493831525840.3154462320573.072242920682.49665757528-1.481800992843.11960197344-0.1368575277310.2750532311180.2485613842880.02608621102250.0472624171832-0.0936117531644-0.08707921203130.06377724859830.06425501230090.0666942122770.001669637110850.02077161771270.0605644303345-0.007116958181610.06261327798014.9078354002711.79284944986.9099650825
73.11264345004-3.181023472050.2180969180573.4593747864-0.3525780569760.903753799721-0.0519169978958-0.09849106337330.02525279543740.06116999430360.00167954486126-0.175003580152-0.008950700927720.0519721707110.02151223621730.0617178557971-0.0212961416672-0.0008084238984310.0568617304350.007058079706960.092610559260714.433365654811.563139447331.8491833386
85.32322224579-3.130415563581.118503713524.16319193879-0.1302859037570.4082997194180.0382239338141-0.003767353524550.101236821475-0.185293189040.0010243873588-0.0608034100325-0.0516618555040.0522440713872-0.02010710963740.0737715882668-0.0213442790470.01440684658410.07990760256750.004876157483650.056039828749922.342114286319.50119732929.4231759461
93.51230237202-3.489345537623.582059878855.32276973247-4.289124530316.85281418398-0.0330165593561-0.0918938981472-0.03380301843930.1475603855180.002271307941650.0556462526670.008832764386240.1282576308450.03458234868140.0637372862656-0.02913330705680.01077816023950.07368239220530.008885127684810.052587481841216.285569113816.673682456234.9903000517
107.99418752808-5.861972827935.190024057096.72523312733-3.117277138473.70956017931-0.115629783176-0.1607750182270.09531814249240.06859872701990.0561250441277-0.0961244287314-0.0914520408932-0.06308812699420.06467835186860.0737938715703-0.02337125936380.01496216671260.07245295554740.01400760818480.049766205005311.596162516717.228575031531.8389922369
117.17437731444-3.074221164392.442085509661.60011332654-0.8002900504690.9787364566610.09245294945740.169927638603-0.168312864485-0.0752074717314-0.05713552949650.06453386352680.001399055909740.0427630453511-0.03701246637580.092082988161-0.02163574968940.008333693372330.09928354456610.003952998498450.072015392646116.819550519614.449901283121.9128439471
125.88858379736-5.6277593536-2.293216129595.55687109931.806179499641.4906992783-0.0522108625237-0.179281790503-0.3483854263210.04418842200020.009366666946840.04839370641920.04280885528350.03309075135830.04554218764190.0706929131263-0.0191834404933-0.01213165401760.07553276698270.01303079163050.11743592895714.33163862787.8607559611229.3099117178
137.49003279535-0.1673926230471.453940599082.43227982521.535864958142.37418187868-0.0811430652752-0.3489454822220.4787948061830.0379648948813-0.002631091296920.0661920101965-0.0663331253367-0.03341166376340.0597968540450.110007254555-0.004956444961250.01265266320280.08518049845370.0007784627108210.075244601361311.122093192224.364051265234.8678305765
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 10 )AA1 - 101 - 10
22chain 'A' and (resid 11 through 40 )AA11 - 4011 - 40
33chain 'A' and (resid 41 through 48 )AA41 - 4841 - 48
44chain 'A' and (resid 49 through 59 )AA49 - 5949 - 59
55chain 'A' and (resid 60 through 76 )AA60 - 7660 - 76
66chain 'A' and (resid 77 through 87 )AA77 - 8777 - 87
77chain 'B' and (resid 1 through 10 )BC1 - 101 - 10
88chain 'B' and (resid 11 through 26 )BC11 - 2611 - 26
99chain 'B' and (resid 27 through 40 )BC27 - 4027 - 40
1010chain 'B' and (resid 41 through 48 )BC41 - 4841 - 48
1111chain 'B' and (resid 49 through 66 )BC49 - 6649 - 66
1212chain 'B' and (resid 67 through 76 )BC67 - 7667 - 76
1313chain 'B' and (resid 77 through 87 )BC77 - 8777 - 87

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